If the protein aggregated due to the hydrophobic effect you wont be able to redissolve it. did you purify it from somewhere?

Dilute the sample and stir it for some time. After that, centrifuge it to remove any undissolved protein and carefully take the supernatant that contain soluble protein. U may even try this repeatedly and optimize the storage conditions for your protein.

Hi Meng, try using a sonicating waterbath to bring the precipitate into solution.

If that doesn't work, check the pH of the protein solution. If the pH is close to the protein pI, then you need to adjust the pH. 

Either you have a concentrated solution (you reach saturation conditions at 4 C) and need to dilute it or the buffer was not properly selected.

Thank you very much.  I found no target protein in the MS result of the supernatant. And the precipitation can't dissolve in the range from pH 3.0 to 12.0, I tried ultrasonic, waterbath, some organic solvent, they are all noneffective. Maybe there was some thing wrong in my operation. 

If the protein aggregated due to the hydrophobic effect you wont be able to redissolve it. did you purify it from somewhere?

In case of aggregated condition, as pointed out by Omar, you may try using either of the two methods discussed in one of our papers. Hope this may be of help!!!

https://www.ncbi.nlm.nih.gov/pubmed/26514067

If your protein has free -SH group(s) (Cys), then it could be forming C-C crosslinked precipitates..

You could try 8M Urea or 6M Guanidine. Though these will denature your protein. So it depends on how you wish to use the protein.

There is a pair of -SH group in my protein, and they should be forming C-C in the renaturation phase. Why the hydrophobic effect impact solubility? Can you tell me more about about? Thank you very much. I down loaded the paper, I will read it later. I am not sure if the Urea or Guanidine suitable for my protein, we want to purify the protein and it must be active. By the way, how can I reply your answer respectively?

Run a non-reducing SDS PAGE and a reducing SDS PAGE on your sample.

That should answer the question whether the precipitate is C-C crosslinked or bound together by hydrophobicity. 

if it is an inclusion body, just try to dissove it in urea/guanidine-HCl and regain the native state by diluting in pulse. that will slowly decrease the urea/gu conc. without misfolding.